Read Skyline exported files

read_skyline(files)

Arguments

files

Character vector with filepaths to Skyline exported files in CSV format.

Value

LipidomicsExperiment object.

Examples

datadir <- system.file("extdata", package = "lipidr") # all csv files filelist <- list.files(datadir, "data.csv", full.names = TRUE) d <- read_skyline(filelist)
#> Successfully read 3 methods. #> Your data contain 58 samples, 10 lipid classes, 277 lipid molecules.
# View automatically generated lipid annotations rowData(d)
#> DataFrame with 279 rows and 26 columns #> filename Molecule Precursor.Mz Precursor.Charge Product.Mz #> <character> <character> <numeric> <integer> <numeric> #> 1 A1_data.csv PE 32:0 692.5 1 551.5 #> 2 A1_data.csv PE 32:1 690.5 1 549.5 #> 3 A1_data.csv PE 32:2 688.5 1 547.5 #> 4 A1_data.csv PE 34:1 718.5 1 577.5 #> 5 A1_data.csv PE 34:1 NEG 716.5 1 196 #> ... ... ... ... ... ... #> 275 F2_data.csv PC(P-40:3) 824.6 1 184.1 #> 276 F2_data.csv PC(P-40:4) 822.6 1 184.1 #> 277 F2_data.csv PC(P-40:5) 820.6 1 184.1 #> 278 F2_data.csv PC(P-40:6) 818.6 1 184.1 #> 279 F2_data.csv 15:0-18:1(d7) PC 753.615 1 184.07 #> Product.Charge clean_name ambig not_matched istd class_stub #> <integer> <factor> <logical> <logical> <logical> <character> #> 1 1 PE 32:0 FALSE FALSE FALSE PE #> 2 1 PE 32:1 FALSE FALSE FALSE PE #> 3 1 PE 32:2 FALSE FALSE FALSE PE #> 4 1 PE 34:1 FALSE FALSE FALSE PE #> 5 1 PE 34:1 FALSE FALSE FALSE PE #> ... ... ... ... ... ... ... #> 275 1 PCP-40:3 FALSE FALSE FALSE PCP #> 276 1 PCP-40:4 FALSE FALSE FALSE PCP #> 277 1 PCP-40:5 FALSE FALSE FALSE PCP #> 278 1 PCP-40:6 FALSE FALSE FALSE PCP #> 279 1 PC 15:0-18:1(d7) FALSE FALSE TRUE PC #> chain1 l_1 s_1 chain2 l_2 s_2 chain3 #> <character> <integer> <integer> <character> <integer> <integer> <character> #> 1 32:0 32 0 NA NA #> 2 32:1 32 1 NA NA #> 3 32:2 32 2 NA NA #> 4 34:1 34 1 NA NA #> 5 34:1 34 1 NA NA #> ... ... ... ... ... ... ... ... #> 275 40:3 40 3 NA NA #> 276 40:4 40 4 NA NA #> 277 40:5 40 5 NA NA #> 278 40:6 40 6 NA NA #> 279 15:0 15 0 18:1 18 1 #> l_3 s_3 chain4 l_4 s_4 total_cl total_cs #> <logical> <logical> <character> <logical> <logical> <integer> <integer> #> 1 NA NA NA NA 32 0 #> 2 NA NA NA NA 32 1 #> 3 NA NA NA NA 32 2 #> 4 NA NA NA NA 34 1 #> 5 NA NA NA NA 34 1 #> ... ... ... ... ... ... ... ... #> 275 NA NA NA NA 40 3 #> 276 NA NA NA NA 40 4 #> 277 NA NA NA NA 40 5 #> 278 NA NA NA NA 40 6 #> 279 NA NA NA NA 33 1 #> Class #> <character> #> 1 PE #> 2 PE #> 3 PE #> 4 PE #> 5 PE #> ... ... #> 275 PC #> 276 PC #> 277 PC #> 278 PC #> 279 PC